#######################################################
# mandatory variables
#######################################################
# SAMPLE should be a data frame, row names must be sample id and there must be a
# 'subgroup' column which corresponds to classes of samples. There can also
# be other annotation columns.
SAMPLE = data.frame(subgroup = ..., ...)
rownames(SAMPLE) = ...
# COLOR: a list of color settings corresponding to annotation column in
# 'SAMPLE'. The value of each list element must be either a named vector
# or a color mapping function. 'COLOR$subgroup' must be defined or random color
# will be assigned. Names of other color settings should be same as
# corresponding columns in 'SAMPLE'.
COLOR = list(subgroup = c(...), ...)
# CHROMOSOME: a vector of chromosome names.
CHROMOSOME = paste0("chr", 1:22)
# GENOME: abbreviation of species.
GENOME = "hg19"
# PROJECT_DIR: path of output directory. Several sub directories will be created.
PROJECT_DIR = ...
# GENOMIC_FEATURE_LIST: a list of genomic features as GRanges objects. There
# must be a element named 'cgi' and 'cgi_shore' will be added accordingly.
# If `TXDB` is provided, gene, exon, intron, tss, intergenic
# will be added automatically.
GENOMIC_FEATURE_LIST = list(
cgi = ...
)
# how to get the object which stores data by chromosome
methylation_hooks$get_by_chr = function(chr) {
...
obj = list(gr = ...,
raw = ...,
cov = ...,
meth = ...)
return(obj)
})
#######################################################
# optional variables
#######################################################
# TXDB (optional): a `GenomicFeatures::TxDb` object.
library(GenomicRanges)
TXDB = loadDb(...)
# GTF file which is used to build 'TXDB'. If it is null, `metadata(TXDB)[3, "value"]` will be used
GTF_FILE = ...
# EXPR (optional): a matrix which contains expression values. Column names
# should be sample id and row names should be gene ids. Note gene ids in the
# expression matrix should be same type as genes in `GenomicFeatures::TxDb`.
EXPR = ...
# MARKS (optional): a vector of ChIP-Seq markers.
MAKRS = c(...)
# chipseq_hooks() is optional unless you want to do integrative analysis.
chipseq_hooks$sample_id = function(mark) {
})
chipseq_hooks$peak = function(mark, sid, ...) {
})
chipseq_hooks$chromHMM = function(sid, ...) {
})
CGI_SHORE_EXTEND = 2000
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.